CPPTRAJ cookbook

Recipes and examples to perform analysis using CPPTRAJ.

In addition to the series of recipes, we present a list of fast one-liner CPPTRAJ codes that can be useful in the day to day work for the computational chemist.

All the recipes presented for CPPTRAJ can be run by saving the commands in a text file (i. e. with the name: in.cpptraj) and then executing in the comand line:

cpptraj -i in.cpptraj

Recipes index.

Combining multiple trajectory files into a single trajectory and remove water molecules to save space

Creating a hydrogen-mass repartitioned topology

Reading the OUT files and plotting different properties

Create an ensemble of PDBs from a trajectory

Generating histograms with CPPTRAJ

Histogram analysis of dihedral angle distributions

Hydrogen bond analysis within a protein

Hydrogen bond analysis between a protein and a small molecule

Comparing the structural difference between a series of ligand-protein complex

Detect regions of high mobility in a protein simulation.

Filtering frames based on a distance and creating a new filtered trajectory

Calculate states between a small molecule and a receptor

Clustering a protein simulation from multiple independent copies

Making a 3D histogram of the position of a small molecule around a receptor

Reorienting small molecules to fit the orientation of another molecule

Detect amino acid interactions between a protein receptor and a small peptide

Mapping Ion Density onto Multidomain Complexes

Calculating the radial distribution function of ions around a biomolecule

Compare the surface area of two cyclic peptides

Measure the stacking percentage of a protein-ligand complex

Create a new AMBER-compatible nucleotide to perform MD simulations